Downloading: s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Sequence/WholeGenomeFasta/Homo_sapiens_assembly38.fasta
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/19/35073f0f3911f6f18bbaaa99d38a74/.command.sh
  Downloading: s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Sequence/WholeGenomeFasta/Homo_sapiens_assembly38.fasta.fai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/fd/8abc314a974814425109414af99c6a/HCC1395_tumor/HCC1395_tumor_R2.fastq.gz
  Downloading: s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Sequence/BWAIndex
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/19/35073f0f3911f6f18bbaaa99d38a74/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/fd/8abc314a974814425109414af99c6a/HCC1395_tumor/HCC1395_tumor_R1.fastq.gz
==> STAGING COMPLETE (7 inputs)

cmdline: /opt/conda/share/sentieon-202308.03-3/libexec/util sort -r Homo_sapiens_assembly38.fasta -t 31 -o HCC1395_tumor.bam --sam2bam -
This software is licensed to bgold@natera.com by Sentieon Inc.
This software is licensed to bgold@natera.com by Sentieon Inc.
version: sentieon-genomics-202308.03
[M::bwa_idx_load_from_disk] read 3171 ALT contigs
[M::main_mem] bwa index loaded in 1618.285 CPU sec, 57.806 real sec
[M::process] read 124464 sequences (17920568 bp) in 0.168 CPU sec, 0.173 real sec...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 43611, 0, 5)
[M::mem_pestat] skip orientation FF as there are not enough pairs
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (180, 272, 391)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 813)
[M::mem_pestat] mean and std.dev: (297.21, 149.05)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 1024)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] skip orientation RR as there are not enough pairs
[M::mem_process_seqs] Processed 124464 reads in 20.128 CPU sec, 0.667 real sec
os version: Linux 6.12.83
cpu vendor: GenuineIntel
 signature: 000a06d1
  features: 1f8bfbff fffab20b
  extended: f1bf27eb 1b407f7e
  amd bits: 2c100800 00000121
     brand: Intel(R) Xeon(R) 6975P-C
threads: 31
algo: bwa-mem
license: sentieon:klib=31
reads: 124464
overall: 68518805504 mem 1484.730 user 158.796 sys 63.589 real
[main] Version: 0.7.17-r1188
[main] CMD: /opt/conda/share/sentieon-202308.03-3/libexec/bwa mem -K 100000000 -Y -R @RG\tID:REGRESSION.HCC1395_tumor.L003\tPU:L003\tSM:HCC1395_tumor\tLB:HCC1395_tumor\tDS:s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Sequence/WholeGenomeFasta/Homo_sapiens_assembly38.fasta\tPL:ILLUMINA -t 31 ./BWAIndex/Homo_sapiens_assembly38.fasta.64 HCC1395_tumor_R1.fastq.gz HCC1395_tumor_R2.fastq.gz
[main] Real time: 63.626 sec; CPU: 1643.528 sec
sorting block 0, #reads = 124643 mem = 59577413 peak = 166858752
uniq header count 1
merging 1 blocks
sw version: sentieon-genomics-202308.03
os version: Linux 6.12.83
cpu vendor: GenuineIntel
 signature: 000a06d1
  features: 1f8bfbff fffab20b
  extended: f1bf27eb 1b407f7e
  amd bits: 2c100800 00000121
     brand: Intel(R) Xeon(R) 6975P-C
threads: 31 max 192
algo: util-sort
license: sentieon:util=1
output file size: 7263380
output reads: 124643
bam_mem_sort: 1 calls 0.026 user 0.000 sys 0.027 real
bam_write: 1 calls 0.080 user 0.000 sys 0.082 real
execute: 1 calls 0.062 user 0.104 sys 63.986 real
merge_files: 1 calls 0.047 user 0.082 sys 0.241 real
parse_chunk: 2 calls 0.054 user 0.009 sys 0.071 real
read_chunk: 7 calls 0.039 user 0.022 sys 5.061 real
sort_block: 1 calls 0.161 user 0.022 sys 5.086 real
write_chunk: 3 calls 0.003 user 0.012 sys 0.026 real
overall: 473063424 mem 1.303 user 0.156 sys 64.011 real
ls: cannot access '*.cram': No such file or directory